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Just like any other operating system, GNU/Linux also stores its most important configuration files using various ways. Some are embedded into the root directory itself... but as everyone knows, the desktop and the Kernel are separately developed in GNU/Linux, both Gnome and KDE desktops (including other of course) store their user configuration files separately.

Concerning the GTK written Gnome, it stores its main configurations such as menus, window behaviors (you know, what should happen when you right-click on the title bar or its button layout, etc), default fonts and their sizes, applications and their assigned extensions (such as Totem for both playing and creating video thumbnails for various formats, etc), default icons for applications are just a few to mention...

... this database is managed in Gnome by using an application called "GConf-Editor". Now whenever you install a new program in Gnome (say in Ubuntu Linux) then those applications automatically use Gconf-editor as a way of applying their settings such as integrating into the main menu in the desktop, etc across all the users for instance.

So as you can see the more apps that you install the more settings are added. Although whenever you uninstall these apps, they do remove those Gconf entries but since nothing is perfect, some portions of these applications can still be "left inside" in Gconf database thus slow downing your Gnome desktop!.

Finally!, something useful :)...

It is obviously not possible to manually check each entry and clean it all by hand and on the other hand the average users (like you and me :D) won't have enough knowledge even to think about doing something like that either.

In that sense, there is a GUI tool written in GTK+ toolkit called "Gconf Cleaner" that does exactly that. It first scans your Gnome Gconf-database/registry and identifies the entries that are no longer used by applications. So all you gotta do is just press a button, and it'll clean all those unused entries within seconds!.

However, I couldn't save these settings :/, it just crashed, could be a bug...

If you use Ubuntu 11.04 Natty Narwhal (should work in 10.04 and 10.10 as well) then you can install Gconf Cleaner by entering the below command in your Terminal.

sudo apt-get install gconf-cleaner

Once installed you can run it by pressing "Alt" + "F2" keys and entering the below command in that box or in Unity dash.

gconf-cleaner

+ It can also be launched via: "Applications" -> "System Tools", in the classic Gnome desktop if you like.

I don't use Unity desktop much but since it uses the Gconf-editor, not only on the classic Gnome desktop but this should clean entries in Unity as well.

Note: I don't know if it's a bug, but when I tried to save my gconf settings, the app just crashed. Although I can click on the forward button and clean the entries... but since you can't create a backup... use it at your own risk.